1. Field of the Subject Disclosure
The present subject disclosure relates to imaging for medical diagnosis. More particularly, the present subject disclosure relates to comprehensive multi-assay tissue analysis.
2. Background of the Subject Disclosure
In the analysis of biological specimens such as tissue sections, blood, cell cultures and the like, biological specimens are mounted on slides and stained with one or more combinations of stain and biomarkers, and the resulting assay is viewed or imaged for further analysis. Observing the assay enables a variety of processes, including diagnosis of disease, assessment of response to treatment, and development of new drugs to fight disease. An H&E assay includes two stains (Hematoxylin and Eosin) that identify tissue anatomy information (cell nuclei and proteins, respectively). A special staining assay identifies target substances in the tissue based on their chemical character, biological character, or pathological character. An immunohistochemistry (IHC) assay includes one or more stains conjugated to an antibody that binds to protein, protein fragments, or other structures of interest in the specimen, hereinafter referred to as targets. The antibodies, other compounds, or substances that bind a target in the specimen to a stain are referred to as biomarkers in this subject disclosure. For an H&E or a special staining assay, biomarkers have a fixed relationship to a stain (e.g., the often used counterstain hematoxylin), whereas for an IHC assay, a choice of stain may be used for a biomarker to develop and create a new assay. Biological specimens such as tissue sections from human subjects are prepared according to an assay before imaging. Upon applying a single light source, a series of multiple light sources, or any other source of input spectra to the tissue, the assay can be assessed by an observer, typically through a microscope, or image data can be acquired from the assay for further processing. In such an acquisition, multiple channels of image data, for example color channels, are derived, with each observed channel comprising a mixture of multiple signals. Processing of this image data can include methods of color separation, spectral unmixing, color deconvolution, etc. that are used to determine a local concentration of specific stains from the observed channel or channels of image data. For image data processed by automated methods, depicted on a display, or for an assay viewed by an observer, a relation may be determined between the local appearance of the stained tissue and the applied stains and biomarkers to determine a model of the biomarker distribution in the stained tissue.
However, the prior art does not disclose an efficient method or system for querying multiple biomarkers in a multiplex assay, particularly in cases where contextual information about the tissue specimen, anatomical detail information, and co-location information is relevant to the analysis. A representative example is the case of tumor heterogeneity, wherein one or more cancerous glands may be caused by or propagated due to a variety of reasons. In other words, cancer is becoming known to be a multi-disease state, and tumors can grow cancerous for multiple reasons. For a surgically-extracted tissue block including a tumor gland, items of interest queried from the specimens could indicate which therapies are likely or promising. A combination of macro tissue information with microanatomical definitions may be required prior to analyzing the biomarkers. The cells of interest may include, for instance, tumor cells, normal tissue epithelium, stromal cells, vascular cells, and immune cells. A multitude of immune cells and immune cell differentiations may need to be queried for a comprehensive immune assay. For instance, while performing a tumor microenvironment assessment, different biomarkers are known that indicate the presence of different cells and their differentiation in and around a tumor. A left half of a tumor may have a different genetic makeup than the right half. For breast cancer patients, a standard breast panel includes slides stained with assays including estrogen/progesterone receptors, proliferation markers, etc. The combined location and intensity of different cells in the tissue and/or tumor cells with different expression, for example, gene or protein expression, separated into different anatomical regions, would be indicative of general and therapy-dependent patient prognosis.
Present methods for multiplex IHC staining involve imaging with fluorescent or brightfield multi-spectral imagers to provide rich input to determine the presence and co-location of the stains within the same tissue. However, such assays are not readily available as they require non-standard staining and imaging techniques and equipment. An increase in a number of queried biomarkers further complicates the analysis. Multiple assays or stains are required to identify each of the cells and their differentiation in a tumor microenvironment as well as the anatomic structures themselves. Moreover, manual outlining of the same region of tissue on multiple input images is labor-intensive, tedious, and error-prone, and therefore not considered commercially viable. Today's analyses are therefore limited to one or a few biomarkers queried on a single slide, or on multiple markers on multiple slides taken from the same tissue. Generally, a qualitative or visual assignment of anatomical context is often left to an observer who has to repeat this step on each slide. However, simply looking at individual results will result in therapy selection that does not target all parts of the tumor as this might not reflect heterogeneous regional or anatomical differences of the biomarker distribution in a tumor.